|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
1-396 |
2.30e-121 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 377.37 E-value: 2.30e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKkasss 80
Cdd:PRK08565 325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR----- 399
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 81 kAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGSPLI 160
Cdd:PRK08565 400 -TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 161 DFMRQRGMDLLEEYDPVMNPRATKVMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTI--IRDVREREIRVFTDAGRV 238
Cdd:PRK08565 479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 239 CRPLFVVDNdpkssnrGNLVLKQEQVERLQndqeilanlegvseeereKSIYGWKGLVDEGVVEYLDAEEEETAMITMTP 318
Cdd:PRK08565 559 RRPLIVVEN-------GKPKLTREHVEKLK------------------KGELTFDDLVKMGVIEYLDAEEEENAYVALDP 613
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580878 319 EDL-EEHknmragiqyddaredphrrikpkpnasvriwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:PRK08565 614 EDLtPEH-------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-396 |
5.55e-80 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 262.89 E-value: 5.55e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKKaSSS 80
Cdd:cd00653 231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRF-LMQ 309
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 81 KAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpgspl 159
Cdd:cd00653 310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 160 idfmrqrgmdlleeydpvmnpratkvmlngtwvgvhrnaghladtlrslrrkgllsfevtiirdvrereirvftdaGRVC 239
Cdd:cd00653 382 ----------------------------------------------------------------------------GRIE 385
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 240 RPLFVVDNDpkssnrgnlvlkqeqverlqndqeilanlegvseeereksiygwkglvdegvveyldaeeeetamitmtpe 319
Cdd:cd00653 386 RPYRIVEKE----------------------------------------------------------------------- 394
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878 320 dleehknmragiqyddaredphrrikpkpnasvriWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:cd00653 395 -----------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG 436
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
1-396 |
1.55e-40 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 153.34 E-value: 1.55e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLhrcvETGREFNITLA--VKTNIITSGLRYCLATGnwgdqkkas 78
Cdd:COG0085 303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERM----TTQDVEAITPQslINIRPVVAAIKEFFGSS--------- 369
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 79 sskaGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYV 150
Cdd:COG0085 370 ----QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV 441
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 151 TvgtpgsplidfmrqrgmdlleEYdpvmnpratkvmlngtwvgvhrnaghladtlrslrrkgllsfevtiirdvrereir 230
Cdd:COG0085 442 N---------------------EY-------------------------------------------------------- 444
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 231 vftdaGRVCRPLFVVDNdpkssnrgnlvlkqeqverlqndqeilanlegvseeereksiygwkGLVDEGvVEYLDAEEEE 310
Cdd:COG0085 445 -----GFIETPYRKVEN----------------------------------------------GKVTDE-IEYLTADEEE 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 311 TAMITMTPEDLEEHKNmragiqYDDAREDPHRRIKPKPNASVRIwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAM 390
Cdd:COG0085 473 NYYIAQANAPLDEDGN------FLEERVLVRYRGEEVLVPPEEV-DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANM 545
|
....*.
gi 954580878 391 GKQAMG 396
Cdd:COG0085 546 QRQAVP 551
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
86-149 |
1.41e-31 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 114.16 E-value: 1.41e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878 86 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 149
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
|
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
1-396 |
2.30e-121 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 377.37 E-value: 2.30e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKkasss 80
Cdd:PRK08565 325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR----- 399
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 81 kAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGSPLI 160
Cdd:PRK08565 400 -TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 161 DFMRQRGMDLLEEYDPVMNPRATKVMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTI--IRDVREREIRVFTDAGRV 238
Cdd:PRK08565 479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 239 CRPLFVVDNdpkssnrGNLVLKQEQVERLQndqeilanlegvseeereKSIYGWKGLVDEGVVEYLDAEEEETAMITMTP 318
Cdd:PRK08565 559 RRPLIVVEN-------GKPKLTREHVEKLK------------------KGELTFDDLVKMGVIEYLDAEEEENAYVALDP 613
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580878 319 EDL-EEHknmragiqyddaredphrrikpkpnasvriwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:PRK08565 614 EDLtPEH-------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-396 |
5.55e-80 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 262.89 E-value: 5.55e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKKaSSS 80
Cdd:cd00653 231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRF-LMQ 309
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 81 KAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpgspl 159
Cdd:cd00653 310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 160 idfmrqrgmdlleeydpvmnpratkvmlngtwvgvhrnaghladtlrslrrkgllsfevtiirdvrereirvftdaGRVC 239
Cdd:cd00653 382 ----------------------------------------------------------------------------GRIE 385
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 240 RPLFVVDNDpkssnrgnlvlkqeqverlqndqeilanlegvseeereksiygwkglvdegvveyldaeeeetamitmtpe 319
Cdd:cd00653 386 RPYRIVEKE----------------------------------------------------------------------- 394
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878 320 dleehknmragiqyddaredphrrikpkpnasvriWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:cd00653 395 -----------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG 436
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
181-396 |
9.66e-50 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 176.69 E-value: 9.66e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 181 RATKVMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVDNdpkssnrGNLVLK 260
Cdd:PRK07225 3 RKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLT 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 261 QEQVERLQNDqEIlanlegvseeereksiyGWKGLVDEGVVEYLDAEEEETAMITMTPEDL-EEHknmragiqyddared 339
Cdd:PRK07225 76 EEHIEKLKNG-EL-----------------TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH--------------- 122
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878 340 phrrikpkpnasvriwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:PRK07225 123 ----------------THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLG 163
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
1-167 |
1.43e-48 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 171.67 E-value: 1.43e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWgdqkkaSSS 80
Cdd:PRK09606 328 DDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGG 401
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 81 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGSPLI 160
Cdd:PRK09606 402 RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVK 481
|
....*..
gi 954580878 161 DFMRQRG 167
Cdd:PRK09606 482 EILKELG 488
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
1-396 |
1.55e-40 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 153.34 E-value: 1.55e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLhrcvETGREFNITLA--VKTNIITSGLRYCLATGnwgdqkkas 78
Cdd:COG0085 303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERM----TTQDVEAITPQslINIRPVVAAIKEFFGSS--------- 369
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 79 sskaGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYV 150
Cdd:COG0085 370 ----QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV 441
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 151 TvgtpgsplidfmrqrgmdlleEYdpvmnpratkvmlngtwvgvhrnaghladtlrslrrkgllsfevtiirdvrereir 230
Cdd:COG0085 442 N---------------------EY-------------------------------------------------------- 444
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 231 vftdaGRVCRPLFVVDNdpkssnrgnlvlkqeqverlqndqeilanlegvseeereksiygwkGLVDEGvVEYLDAEEEE 310
Cdd:COG0085 445 -----GFIETPYRKVEN----------------------------------------------GKVTDE-IEYLTADEEE 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 311 TAMITMTPEDLEEHKNmragiqYDDAREDPHRRIKPKPNASVRIwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAM 390
Cdd:COG0085 473 NYYIAQANAPLDEDGN------FLEERVLVRYRGEEVLVPPEEV-DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANM 545
|
....*.
gi 954580878 391 GKQAMG 396
Cdd:COG0085 546 QRQAVP 551
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
86-149 |
1.41e-31 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 114.16 E-value: 1.41e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878 86 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 149
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
185-246 |
1.98e-31 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 113.62 E-value: 1.98e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954580878 185 VMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVD 246
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
292-362 |
4.54e-22 |
|
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.
Pssm-ID: 428013 [Multi-domain] Cd Length: 53 Bit Score: 88.37 E-value: 4.54e-22
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 954580878 292 WKGLVDEGVVEYLDAEEEETAMITMTPEDLEEHKNMRAGIQYddaredphrrikpkpnasVRIWTHCEIHP 362
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREGPY------------------AHTYTHCEIHP 53
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
1-60 |
5.50e-16 |
|
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 78.96 E-value: 5.50e-16
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITS 60
Cdd:pfam04563 337 DDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
369-396 |
3.14e-12 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 67.17 E-value: 3.14e-12
10 20
....*....|....*....|....*...
gi 954580878 369 CASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMG 28
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-145 |
4.31e-11 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 64.94 E-value: 4.31e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFR---LKLQQLVKETKQYLHRCVETGREFNItlaVKTNIITSGLRYCLATGNwgdqkka 77
Cdd:PRK09603 455 DDRDHLGNRRIRAVGELLANELHsglVKMQKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ------- 524
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954580878 78 ssskagVSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK09603 525 ------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
1-145 |
7.35e-09 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 57.79 E-value: 7.35e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVetgrefnITLAVKTNIITSGLRYCLATGNWGdqkkasSS 80
Cdd:CHL00207 298 DDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICD-------IDSLSKFNLINPKPLIALIREFFG------SS 364
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580878 81 KagVSQVLNRYTYASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:CHL00207 365 Q--LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-146 |
2.16e-08 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 56.55 E-value: 2.16e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFR---LKLQQLVKETKQYLHRCVETGREFnITLAVKTNIITSGLryclatgnwgdqkka 77
Cdd:PRK14844 464 DDIDHLGNRRVRSVGEFIENQFRtglLKLERAVVDSMSTSSLDKVSPSDF-INPKVLTNVLRDFF--------------- 527
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954580878 78 SSSKagVSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSL 146
Cdd:PRK14844 528 NSSQ--LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAI 598
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
1-157 |
8.63e-05 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 44.89 E-value: 8.63e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 1 DDRDHFGKKRLDLAGPLMAQVFRL---KLQQLVKETKQYLHRcvetgrefNITLAVKTNIITSGLrycLATgnwgdqkkA 77
Cdd:CHL00001 304 DDIDHLKNKRIRSVADLLQDQFGLalnRLENAVRGTICGAIR--------RKLIPTPQNLVTSTP---LTT--------T 364
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 78 SSSKAG---VSQVLNRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYV 150
Cdd:CHL00001 365 YESFFGshpLSQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHA 442
|
....*..
gi 954580878 151 TVGTPGS 157
Cdd:CHL00001 443 RIGHWGS 449
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
117-145 |
1.62e-04 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 43.94 E-value: 1.62e-04
10 20
....*....|....*....|....*....
gi 954580878 117 RQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK00405 469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
|
|
|